How do I determine a landing position in Kerbal Space Program?

I like Kerbal Space Program. I have a good understanding of space flight and use maneuver nodes to assist.

I'm thinking about working on a multi-part Mün or Minmus station, using multiple ships to drop the base (perhaps several drops) and a rover.

But the difficulty I expect will be landing in the same position repeatably. When I've tested this on Kerbin I'm off, probably because of atmosphere slowing me down.

I watched this video by Scott Manley and he is able to drop items and hit the runway and VAB FROM SPACE!!!

Is there a trick or secret to landing (exactly) where you want?

I think the simplest way to do that (and that's how I usually do) is to use MechJeb with the "land at target" function from orbit. Usually, if your lander is well balanced and not too creative with staging, is quite accurate. One time I actually landed on a previous lander while AFK.

In any case, you can use MechJeb to time the deorbit burn, and then fine tune the landing manually.

If you really don't want to use autopilot, yes, maneuvers nodes don't account for atmosphere, so on Kerbin aim to overshoot your target. Actually, you have try to overshoot your target in any case, because if you don't want to land "Jebediah Kerman style" you're going to brake hard to kill your lateral (first) and vertical velocity before landing.

In the case of Scott Manley's Rods from the Gods videos: lots of trial and error, and a little bit of luck. He mentioned (perhaps in a different video) that he had made several attempts at getting it to hit exactly where he wanted it. Having said that, with each attempt, he refined his approach and the location where he had to perform his deorbit burn such that he could be fairly certain he would hit somewhere at the KSC.

However, calling this a landing would be a bit of a stretch. The things aren't even guided. For atmospheric landings, even having wings and no fuel means you can change course and land where you want (within reason). This was the status-quo for many years in the US manned space program with the shuttles. You still have to time your deorbit burns correctly, but that's dependant a bit on the design, and comes with experience. For landing on a body with little to no atmosphere, you're going to need a powered landing anyway, so as long as you brought enough fuel, at any point in the descent, you'll be able to change your course, and therefore your projected landing location.

As for what descent profile you use, you can go with anything from surface skim (setting your periapse to ~5km above the surface, Scott Manley's favourite) to heaven drop (killing your lateral velocity while at orbital altitudes), and anywhere in between. In all cases, you have to remember that the planet or moon will rotate beneath you. Leave margins for that, and correct your course early and often to save fuel.

Finally, don't think you have to be uber precise on your landings. If you're close, then (with a little practice) you can do a grasshopper jump over the surface and get the various ships that make up your base closer together.